Last data update: 2014.03.03

phyloseq

Package: phyloseq
Version: 1.16.2
Date: 2016-04-16
Title: Handling and analysis of high-throughput microbiome census data
Description: phyloseq provides a set of classes and tools
to facilitate the import, storage, analysis, and
graphical display of microbiome census data.
Maintainer: Paul J. McMurdie <mcmurdie@stanford.edu>
Author: Paul J. McMurdie <mcmurdie@stanford.edu>,
Susan Holmes <susan@stat.stanford.edu>, with
contributions from Gregory Jordan and Scott Chamberlain
License: AGPL-3
Imports: BiocGenerics (>= 0.14.0), ade4 (>= 1.7.2), ape (>= 3.1.1),
biomformat (>= 0.4.0), Biostrings (>= 2.28.0), cluster (>=
1.14.4), data.table (>= 1.9.6), foreach (>= 1.4.2), ggplot2 (>=
2.1.0), igraph (>= 0.7.0), methods (>= 3.1.0), multtest (>=
2.16.0), plyr (>= 1.8), reshape2 (>= 1.2.2), scales (>= 0.3.0),
vegan (>= 2.0.10), Biobase
Depends: R (>= 3.2.0)
Suggests: BiocStyle (>= 1.6), DESeq2 (>= 1.8), genefilter (>= 1.50),
testthat (>= 0.10), knitr (>= 1.10), metagenomeSeq (>= 1.10),
rmarkdown (>= 0.7)
VignetteBuilder: knitr
Enhances: doParallel (>= 1.0.1)
biocViews: Sequencing, Microbiome, Metagenomics, Clustering,
Classification, MultipleComparison, GeneticVariability
URL: http://dx.plos.org/10.1371/journal.pone.0061217
BugReports: https://github.com/joey711/phyloseq/issues
Collate: 'allClasses.R' 'allPackage.R' 'allData.R' 'as-methods.R'
'show-methods.R' 'plot-methods.R' 'extract-methods.R'
'almostAllAccessors.R' 'otuTable-class.R' 'phyloseq-class.R'
'taxonomyTable-class.R' 'IO-methods.R' 'merge-methods.R'
'multtest-wrapper.R' 'ordination-methods.R'
'transform_filter-methods.R' 'validity-methods.R'
'assignment-methods.R' 'sampleData-class.R' 'extend_vegan.R'
'network-methods.R' 'distance-methods.R'
'deprecated_functions.R' 'extend_DESeq2.R' 'phylo-class.R'
'extend_metagenomeSeq.R'
RoxygenNote: 5.0.1
NeedsCompilation: no
Packaged: 2016-05-16 03:15:54 UTC; biocbuild

● BiocViews: Classification, Clustering, GeneticVariability, Metagenomics, Microbiome, MultipleComparison, Sequencing
● 63 images, 131 functions, 1 datasets
● Reverse Depends: 1

Install log

* installing to library '/home/ddbj/local/lib64/R/library'
* installing *source* package 'phyloseq' ...
** R
** data
** inst
** preparing package for lazy loading
** help
*** installing help indices
  converting help for package 'phyloseq'
    finding HTML links ... done
    DPCoA                                   html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/DPCoA.Rd:46: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/DPCoA.Rd:13: missing file link 'phylo'
    JSD                                     html  
    UniFrac-methods                         html  
    finding level-2 HTML links ... done

    access                                  html  
    assign-otu_table                        html  
    assign-phy_tree                         html  
    assign-sample_data                      html  
    assign-sample_names                     html  
    assign-tax_table                        html  
    assign-taxa_are_rows                    html  
    assign-taxa_names                       html  
    build_tax_table                         html  
    capscale-phyloseq-methods               html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/capscale-phyloseq-methods.Rd:36: missing file link 'rda'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/capscale-phyloseq-methods.Rd:40: missing file link 'rda'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/capscale-phyloseq-methods.Rd:65: missing file link 'rda'
    cca-rda-phyloseq-methods                html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/cca-rda-phyloseq-methods.Rd:47: missing file link 'rda'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/cca-rda-phyloseq-methods.Rd:48: missing file link 'capscale.phyloseq'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/cca-rda-phyloseq-methods.Rd:42: missing file link 'rda'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/cca-rda-phyloseq-methods.Rd:57: missing file link 'rda'
    chunkReOrder                            html  
    data-GlobalPatterns                     html  
    data-enterotype                         html  
    data-esophagus                          html  
    data-soilrep                            html  
    decorana                                html  
    dist-class                              html  
    distance                                html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/distance.Rd:45: missing file link 'UniFrac'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/distance.Rd:46: missing file link 'UniFrac'
    distanceMethodList                      html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/distanceMethodList.Rd:14: missing file link 'UniFrac'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/distanceMethodList.Rd:15: missing file link 'UniFrac'
    envHash2otu_table                       html  
    estimate_richness                       html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/estimate_richness.Rd:58: missing file link 'estimateR'
    export_env_file                         html  
    export_mothur_dist                      html  
    extract-methods                         html  
    filter_taxa                             html  
    filterfun_sample                        html  
    fix_phylo                               html  
    gapstat_ord                             html  
    genefilter_sample-methods               html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/genefilter_sample-methods.Rd:49: missing file link 't'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/genefilter_sample-methods.Rd:66: missing file link 't'
    get.component.classes                   html  
    get_sample-methods                      html  
    get_taxa-methods                        html  
    get_taxa_unique                         html  
    get_variable                            html  
    getslots.phyloseq                       html  
    import                                  html  
    import_RDP_cluster                      html  
    import_RDP_otu                          html  
    import_biom                             html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:43: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:51: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:60: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:67: missing file link 'readDNAStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:74: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:163: missing file link 'biom_data'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:165: missing file link 'sample_metadata'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_biom.Rd:167: missing file link 'observation_metadata'
    import_env_file                         html  
    import_mothur                           html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_mothur.Rd:75: missing file link 'phylo'
    import_mothur_constaxonomy              html  
    import_mothur_dist                      html  
    import_mothur_groups                    html  
    import_mothur_otu_table                 html  
    import_mothur_otulist                   html  
    import_mothur_shared                    html  
    import_pyrotagger_tab                   html  
    import_qiime                            html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_qiime.Rd:42: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_qiime.Rd:50: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_qiime.Rd:59: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_qiime.Rd:66: missing file link 'readDNAStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/import_qiime.Rd:73: missing file link 'XStringSet'
    import_qiime_otu_tax                    html  
    import_qiime_sample_data                html  
    import_uparse                           html  
    import_usearch_uc                       html  
    index_reorder                           html  
    intersect_taxa                          html  
    make_network                            html  
    merge_phyloseq                          html  
    merge_phyloseq_pair-methods             html  
    merge_samples-methods                   html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/merge_samples-methods.Rd:45: missing file link 'phylo'
    merge_taxa-methods                      html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/merge_taxa-methods.Rd:33: missing file link 'phylo'
    metaMDS                                 html  
    microbio_me_qiime                       html  
    mt-methods                              html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/mt-methods.Rd:50: missing file link 'mt.minP'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/mt-methods.Rd:54: missing file link 'mt.minP'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/mt-methods.Rd:57: missing file link 'p.adjust.methods'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/mt-methods.Rd:63: missing file link 'mt.minP'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/mt-methods.Rd:67: missing file link 'mt.minP'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/mt-methods.Rd:89: missing file link 'mt.minP'
    nodeplotblank                           html  
    nodeplotboot                            html  
    nodeplotdefault                         html  
    nsamples-methods                        html  
    ntaxa-methods                           html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/ntaxa-methods.Rd:31: missing file link 'phylo'
    ordinate                                html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/ordinate.Rd:35: missing file link 'rda'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/ordinate.Rd:38: missing file link 'capscale.phyloseq'
    otu_table-class                         html  
    otu_table-methods                       html  
    parseTaxonomy-functions                 html  
    pcoa                                    html  
    phy_tree-methods                        html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phy_tree-methods.Rd:8: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phy_tree-methods.Rd:33: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phy_tree-methods.Rd:25: missing file link 'phylo'
    phylo-class                             html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phylo-class.Rd:7: missing file link 'ape'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phylo-class.Rd:12: missing file link 'phylo'
    phylo                                   html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phylo.Rd:12: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phylo.Rd:33: missing file link 'phylo'
    phyloseq-class                          html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phyloseq-class.Rd:12: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phyloseq-class.Rd:40: missing file link 'phylo'
    phyloseq-deprecated                     html  
    phyloseq-package                        html  
    phyloseq                                html  
    phyloseq_to_deseq2                      html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phyloseq_to_deseq2.Rd:26: missing file link 'DESeqDataSetFromMatrix'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/phyloseq_to_deseq2.Rd:60: missing file link 'DESeqDataSetFromMatrix'
    phyloseq_to_metagenomeSeq               html  
    plot_bar                                html  
    plot_clusgap                            html  
    plot_heatmap                            html  
    plot_net                                html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_net.Rd:86: missing file link 'igraph'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_net.Rd:41: missing file link 'layout.auto'
    plot_network                            html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_network.Rd:69: missing file link 'layout.fruchterman.reingold'
    plot_ordination                         html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_ordination.Rd:58: missing file link 'scale_color_manual'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_ordination.Rd:67: missing file link 'scale_shape_manual'
    plot_phyloseq-methods                   html  
    plot_richness                           html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_richness.Rd:36: missing file link 'scale_color_manual'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_richness.Rd:48: missing file link 'scale_shape_manual'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/plot_richness.Rd:127: missing file link 'estimateR'
    plot_scree                              html  
    plot_tree                               html  
    prune_samples-methods                   html  
    prune_taxa-methods                      html  
    psmelt                                  html  
    rank_names                              html  
    rarefy_even_depth                       html  
    read_tree                               html  
    read_tree_greengenes                    html  
    reconcile_categories                    html  
    refseq-methods                          html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/refseq-methods.Rd:8: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/refseq-methods.Rd:33: missing file link 'XStringSet'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/refseq-methods.Rd:25: missing file link 'phylo'
    rm_outlierf                             html  
    sample_data-class                       html  
    sample_data-methods                     html  
    sample_names-methods                    html  
    sample_sums                             html  
    sample_variables                        html  
    show-methods                            html  
    show_mothur_cutoffs                     html  
    splat.phyloseq.objects                  html  
    subset_ord_plot                         html  
    subset_samples-methods                  html  
    subset_taxa-methods                     html  
    tax_glom                                html  
    tax_table-methods                       html  
    taxa_are_rows-methods                   html  
    taxa_names-methods                      html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/taxa_names-methods.Rd:34: missing file link 'phylo'
    taxa_sums                               html  
    taxonomyTable-class                     html  
    threshrank                              html  
    threshrankfun                           html  
    tip_glom                                html  
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/tip_glom.Rd:12: missing file link 'phylo'
Rd warning: /tmp/RtmpoEfoyY/R.INSTALL3e64161d501c/phyloseq/man/tip_glom.Rd:68: missing file link 'phylo'
    topf                                    html  
    topk                                    html  
    topp                                    html  
    transformcounts                         html  
    transpose-methods                       html  
    tree_layout                             html  
** building package indices
** installing vignettes
** testing if installed package can be loaded
* DONE (phyloseq)
Making 'packages.html' ... done

Created & Maintained by Osamu Ogasawara (osamu.ogasawara@gmail.com) and IMSBIO